Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Danio rerio) | AB | ZIRC, Eugene, OR | ZFIN ID: ZDB-GENO-960809–7 | |
| Strain, strain background (Danio rerio) | lmx1bb mutant, ale uchu (jj410 allele) | ZIRC, Eugene, OR, PMID: 17574823 | jj410; ZFIN ID: ZDB-ALT-070426–3 | Schibler and Malicki, 2007 |
| Strain, strain background (Danio rerio) | Tg(actb2:mem-citrine-citrine)hm30 | Megason lab, PMID: 25303534 | hm30; ZFIN ID: ZDB-ALT-150209–1 | Xiong et al., 2014 |
| Strain, strain background (Danio rerio) | Tg(actb2:mem-citrine)/(actb2:Hsa.H2b-tdTomato)hm32 | Megason lab, PMID: 27535432 |
hm32; ZFIN ID: ZDB-ALT-161213–1 |
Aguet et al., 2016 |
| Strain, strain background (Danio rerio) | Tg(actb2:mem-citrine)/(actb2:Hsa.H2b-tdTomato)hm33 | Megason lab, PMID: 27535432 | hm33; ZFIN ID: ZDB-ALT-161213–2 | Aguet et al., 2016 |
| Strain, strain background (Danio rerio) | Tg(−5.0lmx1bb:d2eEGFP)mw10 | gift from Brian Link's lab, PMID: 19500562 | mw10; ZFIN ID: ZDB-ALT-091218–2 | McMahon et al., 2009 |
| Strain, strain background (Danio rerio) | Tg(actb2:mem-mcherry2)hm29 | Megason lab, PMID: 23622240 | hm29; ZFIN ID: ZDB-ALT-130625–1 | Xiong et al., 2013 |
| Strain, strain background (Danio rerio) | Tg(hsp70:rac1_T17N-p2a-mem-cherry2)hm35 | Megason lab, rac1 mutant plasmid gift from Raz lab, this paper | hm35 | Kardash et al., 2010 |
| Strain, strain background (Danio rerio) | Tg(elavl3:GCaMP5G)a4598 | gift from Alexander Schier's lab, PMID: 23524393 | a4598; ZFIN ID: ZDB-ALT-130924–1 | Ahrens et al., 2013 |
| Strain, strain background (Danio rerio) | Tg(actb2:myl12.1-EGFP)e2212 | gift from C.P. Heisenberg's lab, PMID: 25535919 | e2212; ZFIN ID: ZDB-ALT-130108–2 | Compagnon et al., 2014 |
| Strain, strain background (Danio rerio) | Tg(actb2:mCherry-Hsa.UTRN)e119 | gift from C.P. Heisenberg's lab, PMID: 25535919 | e119; ZFIN ID: ZDB-ALT-151029–2 | Compagnon et al., 2014 |
| Antibody | mouse anti ZO-1 | Thermo Fisher Scientific, Waltham, MA | ZO1-1A12 | |
| Antibody | rabbit anti collagen II | Abcam, Cambridge, United Kingdom | ab209865 | |
| Antibody | rabbit anti laminin | Sigma-Aldrich, St. Louis, MO | L9393 | |
| Recombinant DNA reagent | pet-28b-Cas9-His | gift from Alexander Schier's lab, PMID: 24873830 | addgene id: 47327 | Gagnon et al., 2014 |
| Recombinant DNA reagent | pmtb-t7-alpha-bungarotoxin | Megason lab, PMID: 26244658 | addgene id: 69542 | Swinburne et al., 2015 |
| Sequence-based reagent | foxi in situ probes,Danio rerio | PCRtemplate + T7 reaction (Sigma) | RefSeq:NM_181735 | Thisse and Thisse, 2014 |
| Sequence-based reagent | bmp4 in situ probes, Danio rerio | PCRtemplate + T7 reaction (Sigma) | RefSeq:NM_131342 | Thisse and Thisse, 2014 |
| Sequence-based reagent | lmx1bb sgRNA (exon 2), Danio rerio | annealedoligos + SP6 reaction (NEB) | GenBank:CR376762 | Gagnon et al., 2014 |
| Sequence-based reagent | lmx1bb sgRNA (exon 3),Danio rerio | annealed oligos + SP6 reaction (NEB) | GenBank:CR376762 | Gagnon et al., 2014 |
| Peptide, recombinant protein | cas9 protein | Megason lab | purification scheme fromGagnon et al., 2014 | |
| Peptide, recombinant protein | alpha-bungarotoxin | Tocris Bioscience (Bristol, United Kingdom) | Tocris catalog number 2133 | Swinburne et al., 2015 |
| Commercial assay or kit | mMessage mMachine T7 ULTRA kit | Thermo Fisher Scientific, Waltham, MA | AM1345 | |
| Chemical compound, drug | Dextran, Texas Red, 3000 MW | Thermo Fisher Scientific, Waltham, MA | D-3329 | |
| Chemical compound, drug | Dextran, Alexa Fluor 488, 10000 MW | Thermo Fisher Scientific, Waltham, MA | D-22913 | |
| Chemical compound, drug | tricaine methanosulfate | Sigma-Aldrich, St. Louis, MO | E10521 | |
| Chemical compound, drug | nonenyl succinic anhydride | Electron Microscopy Sciences, Hatfield, PA | 19050 | |
| Chemical compound, drug | DMP-30 | Electron Microscopy Sciences, Hatfield, PA | 13600 | |
| Chemical compound, drug | 1,2,7,8-diepoxyoctane (97%) | Sigma-Aldrich, St. Louis, MO | 139564 | |
| Chemical compound, drug | Sorensen's Phosphate Buffer | Electron Microscopy Sciences, Hatfield, PA | 11600–10 | |
| Chemical compound, drug | glutaraldehyde, EM grade | Electron Microscopy Sciences, Hatfield, PA | 16220 | |
| Chemical compound, drug | paraformaldehyde | Electron Microscopy Sciences, Hatfield, PA | 15710 | |
| Chemical compound, drug | potassium ferricyanide | Sigma-Aldrich, St. Louis, MO | 702587 | |
| Chemical compound, drug | osmium tetroxide | Electron Microscopy Sciences, Hatfield, PA | 19140 | |
| Chemical compound, drug | uranyl acetate | Electron Microscopy Sciences, Hatfield, PA | 22400 | |
| Chemical compound, drug | maleic acid | Sigma-Aldrich, St. Louis, MO | m5757 | |
| Chemical compound, drug | acetronitrile | Electron Microscopy Sciences, Hatfield, PA | 10020 | |
| Chemical compound, drug | Taab 812 Resin | Marivac Ltd., Nova Scotia, Canada | ||
| Software, algorithm | MovingROIExtract, convertFormat | https://github.com/krm15/AO-LLSM | ||
| Software, algorithm | ConvertToMegacapture, GoFigure2ContoursToMeshes | https://github.com/krm15/GF2Exchange | ||
| Software, algorithm | Itk-snap |
www.itksnap.org
PMID: 16545965 |
Yushkevich et al., 2006 | |
| Software, algorithm | Fluorender |
www.sci.utah.edu/software/fluorender.html
PMID:23584131 |
Wan et al., 2012 | |
| Software, algorithm | HandBrake | https://handbrake.fr/ | ||
| Software, algorithm | LabVIEW | National Instruments | ||
| Software, algorithm | MATLAB (R2014A) | www.mathworks.com | ||
| Software, algorithm | ParaView | www.paraview.org | ||
| Software, algorithm | GoFigure2 | Xiong et al., 2013 | ||
| Software, algorithm | FIJI (imagJ) |
www.fiji.sc
PMID: 22743772 |
Schindelin et al., 2012 | |
| Software, algorithm | cellPreprocess, multiscalePlanarityAndVoting3D, DistanceFromMask, resample, MorphologicalErosionOnLabelImageFilter, SizeThreshold, MembraneSegmentation, MembraneSegmentationWithMarkersImageFilter, CellSegmentationStatistics | https://github.com/krm15/ACME/tree/MultithreadLookup | ||
| Software, algorithm | Zen software | http://www.zeiss.com/microscopy/us/products/microscope-software/zen-lite.html | ||
| Other | Volcano mould,‘frosted extreme detail’ | https://www.shapeways.com/, this paper | Volcano400 | |
| Other | FemtoJet 4x | Eppendorf, Hamburg, Germany | 5253000017 | |
| Other | Nanoject | Drummond Scientific, Broomall, PA | 3-000-204 | |
| Other | Tungsten wire | Sigma-Aldrich, St. Louis, MO | 267554–9.5G |